Far-Right extremists were a more dangerous threat to national security, it said.

The officers told MPs that Muslims were being “stigmatised” by the Government’s attempts to tackle terrorism, which was adding to “hatred” against entire communities.

In the official intervention, the association said the Government’s anti-terrorism policies could not “continue unchecked”.

The comments, made in a seven-page memorandum to a parliamentary committee investigating extremism, are embarrassing for Gordon Brown. They indicated that Muslim officers may be reluctant to take part in “hearts and minds” anti-terrorism campaigns.

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The organisation, which represents more than 2,000 officers, was previously publicly backed by Mr Brown. The Prime Minister said the association was crucial to bridge the historic divide between Muslims and the police.

There have been growing concerns about the radicalisation of Muslims in Britain. The failed Detroit bombing on Christmas Day was carried out by an al-Qaeda-inspired extremist who had studied in London.

The Daily Telegraph disclosed last week that American intelligence agencies believed that Britain had the greatest number of Islamic extremists of any Western country.

It is thought to be the first time that the Muslim association, which was founded in 2007, has criticised government policy.

In an analysis of the Prevent strategy, which is a set of policies designed to stop radicalisation, the organisation claimed: “The strategies of Prevent were historically focused on so-called Islamist extremism.

“This has subjected the biggest black and ethnic minority community, and second biggest faith group, in an unprecedented manner, stigmatising them in the process.

“Never before has a community been mapped in [such] a manner ... it is frustrating to see this in a country that is a real pillar and example of freedom of expression and choice.

“Our British system is a model for the world to follow, yet we have embarked on a journey that has put this very core of British values under real threat.”

The association warned there were “echoes” of the racism of the 1970s and 1980s which led to inner city riots. “We appear to have ignored the lessons learnt from these dark days,” the officers said.

There is growing criticism among Muslim groups of the government strategy, which was welcomed by mainstream police organisations.

The policies are aimed at stopping Muslims from becoming radicalised through measures such as sponsoring moderate community groups.

Ministers insisted that the strategy, which costs more than £140 million a year, had “real successes”. More than 200 people were convicted of terrorist offences in the past eight years.

But the NAMP claimed the policies had led to “hatred against Muslims” which “has grown to a level that defies all logic and is an affront to British values”.

The organisation said Prevent should focus on confronting far-Right extremists such as the BNP.

The memorandum warned that Muslims were subjected to “daily abuse” due to the strategy. “We must not diminish our British values further by continuing to allow such behaviour and polices to continue unchecked,” it added.

The Muslim officers believe the Government is wrong to blame Islam as the main driver of terrorist activity.

Research by “those convicted of terrorism acts shows Islam was not, and is not, a real driver but all our strategy seem to focus on is this un-evidenced view of Islam being the driver,” they said. The Government said that confronting Islamic terrorism was one of the key priorities of the anti-radicalisation strategy. Last night, the Foreign Office admitted that funding for counter-terrorism policies in Pakistan had been cut.

A spokesman from the Department of Communities and Local Government said: “The idea that we only focus on Muslims on terror issues is completely false.

“Muslims, like other faith groups, engage with government departments right across Whitehall, from health to education to work and pensions, to culture, media and sport. They rightly play a full role in our society, and across public and civic life.”